Mercurial > repos > iuc > sra_tools
comparison sam_dump.xml @ 14:1790dcf3c32d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 30ec06de1f3056967f5cc2d8ef57f9692d5533d7
author | iuc |
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date | Tue, 04 Dec 2018 15:00:55 -0500 |
parents | c38286ea7047 |
children | aad3885b3216 |
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13:c38286ea7047 | 14:1790dcf3c32d |
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1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.3"> | 1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.4"> |
2 <description>format from NCBI SRA</description> | 2 <description>format from NCBI SRA</description> |
3 <macros> | 3 <macros> |
4 <import>sra_macros.xml</import> | 4 <import>sra_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
15 export HOME=\$PWD && | 15 export HOME=\$PWD && |
16 vdb-config --restore-defaults && | 16 vdb-config --restore-defaults && |
17 vdb-config -s "/repository/user/main/public/root=\$PWD" && | 17 vdb-config -s "/repository/user/main/public/root=\$PWD" && |
18 ## Do not use prefetch if region is specified, to avoid downloading | 18 ## Do not use prefetch if region is specified, to avoid downloading |
19 ## the complete sra file. | 19 ## the complete sra file. |
20 #if ( str( $adv.region ) == "" ): | 20 |
21 ASCP_PATH=`command -v ascp` && | 21 #if $input.input_select == "file": |
22 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true && | 22 sam-dump --log-level fatal '${input.file.name}' |
23 prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" && | 23 #else: |
24 ## Duplicate vdb-config, in case settings changed between prefetch and | 24 #if ( str( $adv.region ) == "" ): |
25 ## dump command. | 25 ASCP_PATH=`command -v ascp` && |
26 vdb-config -s "/repository/user/main/public/root=\$PWD" && | 26 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true && |
27 prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" && | |
28 ## Duplicate vdb-config, in case settings changed between prefetch and | |
29 ## dump command. | |
30 vdb-config -s "/repository/user/main/public/root=\$PWD" && | |
31 #end if | |
32 sam-dump --log-level fatal --disable-multithreading | |
27 #end if | 33 #end if |
28 sam-dump --log-level fatal --disable-multithreading | 34 |
29 #if str( $adv.region ) != "": | 35 #if str( $adv.region ) != "": |
30 --aligned-region '$adv.region' | 36 --aligned-region '$adv.region' |
31 #end if | 37 #end if |
32 #if str( $adv.matepairDist ) != "": | 38 #if str( $adv.matepairDist ) != "": |
33 --matepair-distance '$adv.matepairDist' | 39 --matepair-distance '$adv.matepairDist' |
37 #end if | 43 #end if |
38 --header | 44 --header |
39 #if str( $adv.alignments ) == "both": | 45 #if str( $adv.alignments ) == "both": |
40 --unaligned | 46 --unaligned |
41 #end if | 47 #end if |
48 | |
42 #if str( $adv.alignments ) == "unaligned": | 49 #if str( $adv.alignments ) == "unaligned": |
43 --unaligned-spots-only | 50 --unaligned-spots-only |
44 #end if | 51 #end if |
45 #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ): | 52 #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ): |
46 --primary | 53 --primary |
137 | 144 |
138 ------ | 145 ------ |
139 | 146 |
140 **Uploading data for a single accession** | 147 **Uploading data for a single accession** |
141 | 148 |
142 When you type a single accession number (e.g., `SRR1582967`) into **Accession** box and click **Execute** the tool will fetch data for you. As a result you will get a single BAM (or SAM) dataset in the history. | 149 When you type a single accession number (e.g., `SRR1582967`) into **Accession** box and click **Execute** the tool will fetch data for you. As a result you will get a single BAM (or SAM) dataset in the history. |
143 | 150 |
144 ----- | 151 ----- |
145 | 152 |
146 **Uploading multiple datasets using a list of accessions** | 153 **Uploading multiple datasets using a list of accessions** |
147 | 154 |
152 3. Choose uploaded file within the **sra accession list** field | 159 3. Choose uploaded file within the **sra accession list** field |
153 4. Click **Execute** | 160 4. Click **Execute** |
154 | 161 |
155 .. class:: warningmark | 162 .. class:: warningmark |
156 | 163 |
157 BAM datasets produced by this option will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets. | 164 BAM datasets produced by this option will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets. |
158 | 165 |
159 ----- | 166 ----- |
160 | 167 |
161 **Extract data from already uploaded SRA dataset** | 168 **Extract data from already uploaded SRA dataset** |
162 | 169 |
163 If a SRA dataset is present in the history, it can be converted into BAM dataset by setting **select input type** drop-down to *SRA archive in current history*. Just like in the case of extracting data for single accession number a single BAM dataset will be generated in the history. | 170 If a SRA dataset is present in the history, it can be converted into BAM dataset by setting **select input type** drop-down to *SRA archive in current history*. Just like in the case of extracting data for single accession number a single BAM dataset will be generated in the history. |
164 | 171 |
165 @ACCESSION_LIST_HOWTO@ | 172 @ACCESSION_LIST_HOWTO@ |
166 | 173 |
167 ----- | 174 ----- |
168 | 175 |